Genetic Variant ABCC6P1:n.867+12C>T (chr16-18582479-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000546162.6(ABCC6P1):n.867+12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00711 in 146,474 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0071 ( 0 hom., cov: 30)

Exomes 𝑓: 0.0045 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

ABCC6P1
ENST00000546162.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.498

Publications

1 publications found

Variant links:

Genes affected

ABCC6P1 (HGNC:):

ABCC6P1 links:

ABCC6P1 (HGNC:33352): (ATP binding cassette subfamily C member 6 pseudogene 1)

ABCC6P1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000546162.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Variant has high frequency in the NFE (0.0103) population. However there is too low homozygotes in high coverage region: (expected more than 1, got 0).

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546162.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC6P1	NR_003569.1		n.691+12C>T		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ABCC6P1	ENST00000546162.6	TSL:2	n.867+12C>T	intron	N/A
ABCC6P1	ENST00000565566.1	TSL:6	n.656+12C>T	intron	N/A
ABCC6P1	ENST00000565647.7	TSL:4	n.723+12C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00710

AC:

1039

AN:

146384

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00144

Gnomad AMI

AF:

0.00559

Gnomad AMR

AF:

0.00712

Gnomad ASJ

AF:

0.00511

Gnomad EAS

AF:

0.000599

Gnomad SAS

AF:

0.00491

Gnomad FIN

AF:

0.0107

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0109

Gnomad OTH

AF:

0.00706

GnomAD2 exomes

AF:

0.00732

AC:

1118

AN:

152794

AF XY:

0.00748

show subpopulations

Gnomad AFR exome

AF:

0.00138

Gnomad AMR exome

AF:

0.00278

Gnomad ASJ exome

AF:

0.00561

Gnomad EAS exome

AF:

0.000164

Gnomad FIN exome

AF:

0.0147

Gnomad NFE exome

AF:

0.0107

Gnomad OTH exome

AF:

0.00568

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00454

AC:

3514

AN:

773560

Hom.:

Cov.:

AF XY:

0.00461

AC XY:

1875

AN XY:

407042

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000725

AC:

AN:

22084

American (AMR)

AF:

0.00240

AC:

AN:

38674

Ashkenazi Jewish (ASJ)

AF:

0.00336

AC:

AN:

21126

East Asian (EAS)

AF:

0.00118

AC:

AN:

35738

South Asian (SAS)

AF:

0.00251

AC:

174

AN:

69446

European-Finnish (FIN)

AF:

0.00956

AC:

477

AN:

49906

Middle Eastern (MID)

AF:

0.00167

AC:

AN:

4192

European-Non Finnish (NFE)

AF:

0.00502

AC:

2484

AN:

494930

Other (OTH)

AF:

0.00400

AC:

150

AN:

37464

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.254

Heterozygous variant carriers

468

936

1405

1873

2341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

104

156

208

260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00711

AC:

1041

AN:

146474

Hom.:

Cov.:

AF XY:

0.00703

AC XY:

503

AN XY:

71574

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00144

AC:

AN:

40996

American (AMR)

AF:

0.00711

AC:

105

AN:

14774

Ashkenazi Jewish (ASJ)

AF:

0.00511

AC:

AN:

3328

East Asian (EAS)

AF:

0.000600

AC:

AN:

4996

South Asian (SAS)

AF:

0.00492

AC:

AN:

4678

European-Finnish (FIN)

AF:

0.0107

AC:

109

AN:

10144

Middle Eastern (MID)

AF:

0.00

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.0109

AC:

704

AN:

64384

Other (OTH)

AF:

0.00802

AC:

AN:

1996

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.268

Heterozygous variant carriers

109

218

327

436

545

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0161

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.0

(source)

DANN

Benign

0.31

PhyloP100

-0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over